From Harlem

Contents 1 HARLEM - Molecular Modeling Package 1.1 Getting started 2 Download and Install HARLEM on Windows 2.1 To install and execute HARLEM on multiple cores in parallel mode 3 HARLEM Documentation 4 HARLEM Tutorials 5 Useful Python Scripts for HARLEM 6 For Developers 6.1 Projects

[edit] HARLEM - Molecular Modeling Package

HARLEM ( abbreviation stands for HAmiltonians to Research LargE Molecules) is developed by Igor Kurnikov in 1999 while he was a graduate student and a postdoc at the University of Pittsburgh and later at Northwestern University. The first application within HARLEM was developed to study long range electron transfer reactions in biological molecular systems and in nanoelectronic devices. Gradually the scope of the program was extended to incorporate a variety of molecular modeling techniques and approaches. It has been used to study such diverse biological problems as oxidative stress in biology and ionic currents through membrane protein channels.

Currently, HARLEM is a multipurpose multi-scale molecular simulation package with unique capabilities not found in other programs. It also provides convenient graphical interface to a few popular molecular modeling packages such as AMBER and GAUSSIAN.

Currently HARLEM is being actively developed and maintained by Igor Kurnikov and Nikolay Simakov in Maria Kurnikova research group at Carnegie Mellon University in Pittsburgh, PA (USA).

[edit] Getting started

[edit] Download and Install HARLEM on Windows

1. Download harlem.zip

2. Unpack content of harlem.zip file into c: directory, this should create

• directory c://HARLEM with an executable harlem.exe and several dll files
• Subdirectory c://HARLEM/residues_db with residues and force-field databases (currently files amber_94_ff.dat, res_XXX.hlm files)
• Subdirectory c://HARLEM/scripts: with Python scripts providing access to HARLEM classes
• Subdirectory c://HARLEM/basis: with Gaussian Quantum Chemical basis sets in DALTON format
• Subdirectory c://HARLEM/doc: containing HARLEM documentation.
• Subdirectory c://HARLEM/examples with a few input files and scripts to run HARLEM jobs

3. If installation has been performed into the directory other than c: (for example d:\) please set environment variable HARLEM_HOME to this directory (SET HARLEM_HOME=d:\)

4. in c://HARLEM/ execute vcredist_x86_vs_2008_sp1

this completes installation of HARLEM to execute on a single core processor

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[edit] To install and execute HARLEM on multiple cores in parallel mode

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5. in c://HARLEM/ execute mpich2-1.2-win-ia32.msi

this installs the MPICH library of parallel functions

[edit] HARLEM Documentation

• Program Structure
• HARLEM manual and deoxigen documentation

 Beware! currently these pages are old (2004-2006) - 
 they are relevant for the main architecture of the program 
 but there are lots of new features and some discrepancies in class structure etc.

[edit] HARLEM Tutorials

• Molecular Visualization
  • Tutorial 1: Molecular visualization in HARLEM and getting started]

Download and unzip the file. Follow the instructions in the file harlemtutorial.doc

• Molecular Dynamics
  • Tutorial 2: Getting started with Molecular Dynamics and python scripting
• Monte Carlo method
  • Tutorial 3: A simple tutorial for Monte Carlo simulation and python scripting

[edit] Useful Python Scripts for HARLEM

• Overlap Script
  • Scripts:Overlap Script
  • Tutorial:Overlap Script
• Calculation of pKa values
  • Tutorial:pKa Calculations in Parallel using pKaCalcMod

[edit] For Developers

• HARLEM Development and compilation on UNIX

• Compiling Under Windows XP with Microsoft Compilers and autotools

• HARLEM on Linux and Windows, electrostatics via PNPS: PNPS instead of ElectrostMod

Application Programming Interface

 This should contain the link to doxygen documentation

[edit] Projects

1. HIV-RT Project
2. simple_form